DTI Quality Control - Part 2: Tensor fitting

Thursday, March 06, 2014
Do Tromp
0
Comments

After making sure your data was acquired correctly (see also this post) and all looked good - you can go ahead and start tensor fitting. At the core of tensor fitting is using the right gradient directions and sometimes (for programs like Camino) creating a so called "scheme file". A scheme file consists of both the b-values and b-vectors. The b-values are the amount of diffusion weighting used for each volume. Depending on how many non-diffusion weighted or B0 scans you collect (read more on its use here) and what diffusion weighting max you use your b-value file is going to look something like this (shortened version):

0,0,0,0,0,0,1000,1000,1000,1000,1000,1000,1000,1000,1000,1000,1000

Your b-vector are the gradient directions that you collect, often predetermined by the scanner depending on how many total directions you choose to collect. A b-vector file will look something like this (shortened version):

b-vectors

The b-vectors consist out of 3 separate vectors (x, y, z) for each direction acquired. A program like fsl2scheme (more info here) will be able to combine the b-values and b-vectors into a scheme file. Together looking something like this (note that there are 4 b0 slices visible, while the scheme file only shows 1 b0):

Scheme file, next to diffusion volumes

If you run a eddy correction it is advisable to correct your scheme file for the induced movement of each volume after registration. Here are a couple of resources to help you with this:

After running the tensor fitting command you will have to check if the vectors were applied correctly. In the below examples we are using Camino's pdview, but you can use any program that allows you to view the tensors. You should check the axial, coronal and sagittal views. As a reference the corpus callosum can be used, the tensors should follow the shape of the corpus callosum (in red) in a fluid motion, as in the examples below:

Axial view

Coronal view

Sagittal view

EXAMPLES OF WRONG ORIENTATION:

Notice the tensor orientations in corpus callosum (red area)

Wrong orientation

Fix it by adjusting the scheme file:

There are multiple options to correct the scheme file in the fsl2scheme command:

- add -usegradmod(usually when error pops up)

- add -flipx

- add -flipy

- add -flipz

- or any combination of the above, eg. as used in the example above: fsl2scheme -bvecfile bvecs.txt -bvalfile bvals.txt -flipx -flipy -usegradmod prefix.scheme

About This Website

Diffusion-imaging.comgives a comprehensive overview of available software, analyzing methods and research possibilities. Providing background on the tools, methods and software to effectively analyze DTI data. Posts include step-by-step processing and tractography tutorials.

About the developer

Do grew up and went to college in the Netherlands, where she also received her masters degree in Neuroscience & Cognition. She is currently a neuroscience graduate student in the US. Her interest is focused on understanding the neural substrates that underlie normal and abnormal brain functioning. She uses state of the art imaging methods, like magnetic resonance imaging (MRI) and diffusion tensor imaging (DTI) to examine alterations in white-matter structure.

Copyright and Licence

The code on this website is licensed under the GNU 3.0 open source license and you are free to modify and redistribute the code, given that you give others you share the code with the same right, and cite this website and the name of the author.

By reading on you agree to these terms.

For more citable references to the posts on this website visit The Winnower.